Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo).

BACKGROUND: Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting. RESULTS: In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail. CONCLUSIONS: The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity.

Diet, bite force and skull morphology in the generalist rodent morphotype.

For many vertebrate species, bite force plays an important functional role. Ecological characteristics of a species' niche, such as diet, are often associated with bite force. Previous evidence suggests a biomechanical trade-off between rodents specialized for gnawing, which feed mainly on seeds, and those specialized for chewing, which feed mainly on green vegetation. We tested the hypothesis that gnawers are stronger biters than chewers. We estimated bite force and measured skull and mandible shape and size in 63 genera of a major rodent radiation (the myomorph sigmodontines). Analysis of the influence of diet on bite force and morphology was made in a comparative framework. We then used phylogenetic path analysis to uncover the most probable causal relationships linking diet and bite force. Both granivores (gnawers) and herbivores (chewers) have a similar high bite force, leading us to reject the initial hypothesis. Path analysis reveals that bite force is more likely influenced by diet than the reverse causality. The absence of a trade-off between herbivores and granivores may be associated with the generalist nature of the myomorph condition seen in sigmodontine rodents. Both gnawing and chewing sigmodontines exhibit similar, intermediate phenotypes, at least compared to extreme gnawers (squirrels) and chewers (chinchillas). Only insectivorous rodents appear to be moving towards a different direction in the shape space, through some notable changes in morphology. In terms of diet, natural selection alters bite force through changes in size and shape, indicating that organisms adjust their bite force in tandem with changes in food items.

Environment-Assisted Speed-up of the Field Evolution in Cavity Quantum Electrodynamics.

We measure the quantum speed of the state evolution of the field in a weakly driven optical cavity QED system. To this end, the mode of the electromagnetic field is considered as a quantum system of interest with a preferential coupling to a tunable environment: the atoms. By controlling the environment, i.e., changing the number of atoms coupled to the optical cavity mode, an environment-assisted speed-up is realized: the quantum speed of the state repopulation in the optical cavity increases with the coupling strength between the optical cavity mode and this non-Markovian environment (the number of atoms).

Conserving large carnivores: dollars and fence.

Conservationists often advocate for landscape approaches to wildlife management while others argue for physical separation between protected species and human communities, but direct empirical comparisons of these alternatives are scarce. We relate African lion population densities and population trends to contrasting management practices across 42 sites in 11 countries. Lion populations in fenced reserves are significantly closer to their estimated carrying capacities than unfenced populations. Whereas fenced reserves can maintain lions at 80% of their potential densities on annual management budgets of $500 km(-2) , unfenced populations require budgets in excess of $2000 km(-2) to attain half their potential densities. Lions in fenced reserves are primarily limited by density dependence, but lions in unfenced reserves are highly sensitive to human population densities in surrounding communities, and unfenced populations are frequently subjected to density-independent factors. Nearly half the unfenced lion populations may decline to near extinction over the next 20-40 years.

Direct measurement of S-branch N2-H2 Raman linewidths using time-resolved pure rotational coherent anti-Stokes Raman spectroscopy.

S-branch N(2)-H(2) Raman linewidths have been measured in the temperature region 294-1466 K using time-resolved dual-broadband picosecond pure rotational coherent anti-Stokes Raman spectroscopy (RCARS). Data are extracted by mapping the dephasing rates of the CARS signal temporal decay. The J-dependent coherence decays are detected in the time domain by following the individual spectral lines as a function of probe delay. The linewidth data set was employed in spectral fits of N(2) RCARS spectra recorded in binary mixtures of N(2) and H(2) at calibrated temperature conditions up to 661 K using a standard nanosecond RCARS setup. In this region, the set shows a deviation of less than 2% in comparison with thermocouples. The results provide useful knowledge for the applicability of N(2) CARS thermometry on the fuel-side of H(2) diffusion flames.

Beam-induced damage on diffractive hard X-ray optics.

The issue of beam-induced damage on diffractive hard X-ray optics is addressed. For this purpose a systematic study on the radiation damage induced by a high-power X-ray beam is carried out in both ambient and inert atmospheres. Diffraction gratings fabricated by three different techniques are considered: electroplated Au gratings both with and without the polymer mold, and Ir-coated Si gratings. The beam-induced damage is monitored by X-ray diffraction and evaluated using scanning electron microscopy.

Novel opportunities for time-resolved absorption spectroscopy at the X-ray free electron laser.

Time-dependent X-ray Absorption Spectroscopy (XAS) measurements of chemical reaction dynamics have a time resolution which is limited by: (a) the speed and efficiency of the reaction initiation; (b) the duration of the X-ray pulses used for the measurement; and (c) the brightness of the X-ray source. X-Ray Free Electron Lasers (XFEL), which will deliver 20-100 fs pulses of X-rays, with a peak brightness which is 10(10) times that of a synchrotron, will alleviate limitations (b) and (c). Furthermore, by including a synchronized source of UV, visible, IR or THz pump radiation, the XFEL will contribute to the solution of limitation (a). The present article describes the XFEL operating principle and the generic design of an XFEL facility, emphasizing the features of particular interest to the XAS investigator.

Improved data acquisition in grazing-incidence X-ray scattering experiments using a pixel detector.

The use of an area detector in grazing-incidence X-ray experiments lends many advantages in terms of both speed and reliability. Here a discussion is given of the procedures established using the PILATUS pixel detector developed at the Swiss Light Source for optimizing data acquisition and analysis of surface diffraction data at the Materials Science beamline, especially with regard to reflectivity measurements, crystal truncation and fractional order rods, and grazing-incidence diffraction experiments.

Biochemical diagnosis and management of corticosterone methyl oxidase type II deficiency.

Corticosterone methyl oxidase deficiency type II (CMO type II deficiency) is an autosomal recessive disorder characterized by a defect in the terminal step of aldosterone biosynthesis. Previous reports emphasized the diagnostic utility of elevated urinary ratios of 18-hydroxytetrahydro-compound A to tetrahydro-aldosterone, which are primary metabolites of 18-hydroxycorticosterone (18-OHB) and aldosterone, respectively. Limited data suggest that plasma ratios of 18-OHB to aldosterone are also abnormal in affected individuals. We report serum steroid profiles in two siblings with CMO type II deficiency. Serum levels of aldosterone precursors were elevated in both patients before treatment. In particular, the serum ratios of 18-OHB to aldosterone were greatly elevated and declined to normal levels during mineralocorticoid replacement. The possibility of heterozygote detection using this ratio is suggested. We also confirm previous reports of a detrimental effect on linear growth rate after cessation of mineralocorticoid therapy despite maintenance of normal serum electrolytes. This effect is associated with biochemical evidence of chronic salt depletion. Based on our observations, we recommend that serum 18-OHB to aldosterone ratios be routinely measured for the diagnosis and management of patients with CMO type II deficiency.

Clinical aspects of xerostomia.

The physiology of saliva flow and hyposalivation is discussed. Drug-induced hyposalivation results in a higher incidence of dental caries, causes discomfort for denture wearers, and increases the risk of oral infections. Guidelines for preventing and treating drug-induced xerostomia are offered.

Chemical properties, distribution, and physiology of plant and algal carbonic anhydrases.

Plant carbonic anhydrases (CAs) have a range of molecular weights (MW). Among flowering plants, dicotyledons with C3 photosynthesis have two isoenzymes of 140-250K each with 6 subunits, while monocotyledons have two isoenzymes of 42-45K. Plant and animal CAs have a similar amino acid content, subunit size and zinc content, suggesting they are homologous proteins, although the higher plant CAs have no esterase activity and are not strongly inhibited by sulfonamides. Algal CAs vary widely in MW and some are highly sensitive to sulfonamides like the animal enzymes. The two plant isoenzymes, from the chloroplast and cytosol, can be separated by gradient polyacrylamide gel electrophoresis and subsequently visualized by enzymic H+ ion production. In plants, CAs probably facilitate diffusion of CO2 to the site of photosynthetic fixation; they may also have a role in pH regulation, in the use of bicarbonate by aquatic plants and in concentrating inorganic carbon within the chloroplast.

Pancreatitis associated with valproic acid: a review of the literature.

Black box warnings for valproic acid caution clinicians of the potential for fatal hepatotoxicity and teratogenicity. Since 1979, case reports of pancreatitis induced by valproic acid have been published in the medical literature. As a result, pancreatitis was added to the black box warnings for valproic acid. We performed searches of MEDLINE and International Pharmaceutical Abstracts and found valproic acid-induced pancreatitis in 45 patients from 31 published articles. Demographics, clinical characteristics, and outcomes of these patients are summarized. Recommendations for monitoring the potential for pancreatitis to develop in patients receiving valproic acid therapy are described, as are potential mechanisms for inducement of pancreatitis by valproic acid.

The man-eaters with bad teeth.

Two cases of man-eating lions feeding on large numbers of humans (1898, 1991) are discussed. The forensic dental evidence from the lions' remains and eyewitness reports indicate all three lions had serious dental/oral pathology, which may have contributed to their selection of human food over more challenging natural animal prey.

Communication: The electronic structure of matter probed with a single femtosecond hard x-ray pulse.

Physical, biological, and chemical transformations are initiated by changes in the electronic configuration of the species involved. These electronic changes occur on the timescales of attoseconds (10(-18) s) to femtoseconds (10(-15) s) and drive all subsequent electronic reorganization as the system moves to a new equilibrium or quasi-equilibrium state. The ability to detect the dynamics of these electronic changes is crucial for understanding the potential energy surfaces upon which chemical and biological reactions take place. Here, we report on the determination of the electronic structure of matter using a single self-seeded femtosecond x-ray pulse from the Linac Coherent Light Source hard x-ray free electron laser. By measuring the high energy resolution off-resonant spectrum (HEROS), we were able to obtain information about the electronic density of states with a single femtosecond x-ray pulse. We show that the unoccupied electronic states of the scattering atom may be determined on a shot-to-shot basis and that the measured spectral shape is independent of the large intensity fluctuations of the incoming x-ray beam. Moreover, we demonstrate the chemical sensitivity and single-shot capability and limitations of HEROS, which enables the technique to track the electronic structural dynamics in matter on femtosecond time scales, making it an ideal probe technique for time-resolved X-ray experiments.

Two-dimensional structure from random multiparticle X-ray scattering images using cross-correlations.

Knowledge of the structure of biological macromolecules, especially in their native environment, is crucial because of the close structure-function relationship. X-ray small-angle scattering is used to determine the shape of particles in solution, but the achievable resolution is limited owing to averaging over particle orientations. In 1977, Kam proposed to obtain additional structural information from the cross-correlation of the scattering intensities. Here we develop the method in two dimensions, and give a procedure by which the single-particle diffraction pattern is extracted in a model-independent way from the correlations. We demonstrate its application to a large set of synchrotron X-ray scattering images on ensembles of identical, randomly oriented particles of 350 or 200 nm in size. The obtained 15 nm resolution in the reconstructed shape is independent of the number of scatterers. The results are discussed in view of proposed 'snapshot' scattering by molecules in the liquid phase at X-ray free-electron lasers.